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Sample GSM2320279 Query DataSets for GSM2320279
Status Public on May 03, 2017
Title Methyl-FW18
Sample type SRA
Source name retina
Organism Homo sapiens
Characteristics age: fetal week 18
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from retinal tissues using the DNeasy Blood & Tissue Kit (QIAGEN #69504) according to the manufacturer's protocol.
Typically, 2 µg of genomic DNA is used to make WGBS libraries.Whole genome bisulfite sequencing was conducted by the Hudson Alpha research institute for Biotechnology using the Cambridge Epigenetix TrumethylSeq kit (BS workflow) per manufacturer's instructions.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
Data processing Basecalls performed using CASAVA
Whole genome bisulfite sequencing (WGBS) data were mapped to hg19(GRCh37) by BSMAP2.74 with the following parameters: -z 33 -f 5 -g 3 -r 0 -m 17 -x 600 –u.
raw methylation status was called by Bis-SNP (Version 0.82.2).
Based on bis-SNP results, beta-value of non-abolished and non-established CG have been extracted and converted to bigwig for visualization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig
Submission date Sep 19, 2016
Last update date May 15, 2019
Contact name Beisi Xu
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
Platform ID GPL11154
Series (2)
GSE87061 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [WGBS_Hs]
GSE87064 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
BioSample SAMN05787356
SRA SRX2174432

Supplementary file Size Download File type/resource 202.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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